Individual identification in acoustic recordings
Abstract
Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.
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The main bottleneck for individual identification is building and curating reference libraries at a scale that can support global monitoring, along with developing fully automated pipelines that can process such data streams without constant human supervision.
“The main bottleneck, at least for now, is building and curating reference libraries at a scale that can support global monitoring, along with developing fully automated pipelines that can process such data streams without constant human supervision”
From Listening forward: emerging roles of bioacoustics in ecology, evolution, and conservation (2026) · cites this paper as Knight et al. 2024
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“Currently, feature embeddings have made it possible to differentiate adult versus juvenile vocaliza - tions (McGinn et al., 2023 ) and show promise for distinguishing individ - uals (Lakdari et al., 2024 ), a key goal in bioacoustics (Knight et al., 2024 ).”
Integrating AI models into ecological research workflows: The case of terrestrial bioacoustics
Kitzes, J. A., Chronister, L. M., Czarnecki, C., Fiss, C. J., Freeland‐Haynes, L., Goodman, B. D., Lapp, S., Lyon, R. P., Nossan, H., Rhinehart, T. A., et al. (2025) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70133 · Cited by 12 · see citing works
“Fifth, AI models trained to perform individual identification rather than species-level identification could be used to generate marked counts or capture– mark–recapture data (Knight et al., 2024 ).”
Self-citationNational-scale acoustic monitoring of avian biodiversity and migration
Bick, I. A., Bakkestuen, V., Cretois, B., Hillier, B. V., Kålås, J. A., Øien, I. J., Pedersen, M., Raja, K. B., Rosten, C. M., Somveille, M., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-10389-4 · Cited by 9 · see citing works
“Weekly vocalization probability in forested areas across Norway 77 for a , Willow Warbler and b , Spotted Flycatcher shows spatiotemporal species arrival patterns and captures later arrival of Spotted Flycatcher relative to Willow Warbler. c , At eBird survey points, the distribution of aSDM values is signi fi cantly g…”
InfluentialSarkar, E., & Magimai.-Doss, M. (2025) · IEEE International Conference on Acoustics Speech and Signal Processing · doi:10.1109/icassp49660.2025.10889684 · Cited by 5 · see citing works
“In particular, self-supervised learning (SSL) models pre-trained on human speech have shown remarkable success in tackling various bioacoustic tasks, such as animal call-type classification [7]– [11], caller identification [12]–[14], and species recognition [15].”
AI carves out a niche in ecology and conservation research
Gewin, V. L. (2025) · Nature Methods · doi:10.1038/s41592-025-02682-7 · Cited by 7 · see citing works
Lapp, S., Lyon, R. P., Wilson, S. J., Rhinehart, T. A., Czarnecki, C., Chronister, L. M., Fiss, C. J., Larkin, J. L., Bayne, E. M., & Kitzes, J. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.26.661638 · Cited by 6 · see citing works
“Individual vocal recognition (also called acoustic individual identification 9 ) relies on an ‘acoustic signature’, an attribute of a vocalization that is consistently stable within an individual and unique for each individual, which are widespread in vocal animals 8,9 .”
Self-citationKnight, E. C., Wilgenburg, S. L. V., Iles, D. T., Edwards, B. P. M., Yip, D. A., Rhinehart, T. A., Lapp, S., Kitzes, J. A., & Bayne, E. M. (2025) · Ornithological Applications · doi:10.1093/ornithapp/duaf082 · Cited by 6 · see citing works
Self-citationWiniarski, J. M., Whitmore, S. A., Wood, C. E., Eiseman, J. P., Netoskie, E. C., Bieber, M. E., Kramer, H. A., Kelly, K. G., McGinn, K. A., Thompson, C. M., et al. (2026) · Ecological Applications · doi:10.1002/eap.70177 · Cited by 4 · see citing works
“Advances in acoustic individual identification (i.e., distinguishing individuals based on their unique acoustic signature) could also enable the estimation of demographic rates from acoustic recordings in the near future (Knight et al., 2024).”
Acoustic recognition of individuals in closed and open bird populations
Huang, L., Clarke, R. H., Teixeira, D., Chiaradia, A., & Meyer, B. E. (2025) · Ecological Informatics · doi:10.1016/j.ecoinf.2025.103330 · Cited by 8 · see citing works
Goodenough, A. E., & Perks, S. J. (2025) · Journal for Nature Conservation · doi:10.1016/j.jnc.2025.127049 · Cited by 3 · see citing works
Passive Acoustic Data as Phenological Distributions: Uncovering Signals of Temporal Ecology
Clapp, M. K., Tingley, M. W., Lesmeister, D. B., Gremel, S. A., Ransom, J. I., Holmgren, M. L., & Siegel, R. B. (2026) · Ecology and Evolution · doi:10.1002/ece3.73020 · Cited by 4 · see citing works
“…of population biology and behavioral ecology, connecting landscape-scale patterns in PAM-derived data with behavior at the level of species and individuals (Kitzes et al. 2021; McGinn et al. 2023; Knight et al. 2024), and imagining acoustic recordings as a trove of untapped ecological signal.”
Self-citationTary, J. B., Peirce, C., & Hobbs, R. W. (2025) · The Journal of the Acoustical Society of America · doi:10.1121/10.0036223 · Cited by 3 · see citing works
Territorial Acoustic Species Estimation using Acoustic Sensor Networks
Brüggemann, L., Otten, D., Sachser, F., & Aschenbruck, N. (2025) · Ecological Informatics · doi:10.1016/j.ecoinf.2025.103281 · Cited by 3 · see citing works
Dharmarajan, G. (2026) · Animal Behaviour · doi:10.1016/j.anbehav.2026.123547 · Cited by 2 · see citing works
Freeman, B. G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2414224121 · Cited by 2 · see citing works
Acoustic Recognition of Individual Animals in the Presence of Unknown IndividualsPreprint
Huang, L., Clarke, R. H., Teixeira, D., Chiaradia, A., & Meyer, B. E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.18.629284 · Cited by 2 · see citing works
Pérez‐Granados, C., Alonso-Moya, C. D., Barrero, A., Sáez‐Gómez, P., Bota, G., Lahoz‐Monfort, J. J., Osiejuk, T. S., Rogers, A., Schuchmann, K., & Traba, J. (2026) · Scientific Data · doi:10.1038/s41597-026-07131-4 · Cited by 2 · see citing works
Individual Bird Identification by Modeling Temporal Structure in Bioacoustic EmbeddingsPreprint
Gallego-Londoño, J., Martinez-Vargas, J. D., & López, J. D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.21.727031 · Cited by 2 · see citing works
“Although species-level identification is essential for biodiversity monitoring, acoustic data can also provide information about individual-level variation, behavior, and population processes (Knight et al., 2024).”
Upham‐Mills, E. J., Crosby, A. D., Reimer, J. R., Haché, S., Stehelin, T. E., & Bayne, E. M. (2025) · Journal of Wildlife Management · doi:10.1002/jwmg.70026 · Cited by 1 · see citing works
Self-citationPlayback-Based Localization of Songbirds Using Multiple Recorders
Bustamante, L., Gallego-Londoño, J., & López, J. D. (2025) · Communications in computer and information science · doi:10.1007/978-3-032-08206-0_26 · Cited by 1 · see citing works
Guzmán, H. M., Estévez, R. M., Contreras, K., Poveda, H., Sánchez-Galán, J. E., & Merchán, F. (2025) · Frontiers in Marine Science · doi:10.3389/fmars.2025.1661294 · Cited by 1 · see citing works
Zhang, Y., Jiang, X., Zeng, X., Rao, X., & Wang, D. (2025) · Integrative Zoology · doi:10.1111/1749-4877.70040 · Cited by 1 · see citing works
Delgado, G. L., van den Hoogen, J., Dent, D. H., Bradfer‐Lawrence, T., Werden, L. K., Cole, R. J., Quesada, C. D., Fajarado, J.-A. J., Rodríguez, A. M., Solorzano, E. M., et al. (2026) · Global Change Biology · doi:10.1111/gcb.70730 · Cited by 4 · see citing works
“Many modern acoustic studies have sought to identify species within recordings in order to monitor populations, track individual animal movements, or estimate species richness (Kelly et al. 2023; Knight et al. 2024; Ribeiro et al. 2022; Wood et al. 2019).”
Kreuser, A. M., Pendleton, D. E., Record, N. R., & Meyer‐Gutbrod, E. L. (2026) · Limnology and Oceanography Methods · doi:10.1002/lom3.70049 · Cited by 1 · see citing works
“Visual and acoustic surveys can provide presence data with high temporal and spatial resolution (Wells 2018; Knight et al. 2024).”
The role of conservation bioacoustics in achieving global biodiversity goals
Perea, S., Rhinehart, T. A., Bouffaut, L., Araya‐Salas, M., Davidson, I. K., Arcila-Pérez, L. F., Kitzes, J. A., & Buřivalová, Z. (2026) · Nature Reviews Biodiversity · doi:10.1038/s44358-026-00189-3 · Cited by 1 · see citing works
“…durability of CNNs: deep learning frameworks and associated development libraries (such as TensorFlow and PyTorch) evolve rapidly, which may affect year-to-year consistency in analyses, particularly for multi-year time series, raising questions about how best to support stable, long-term workflows.”
Self-citationAcoustic Identification of Individual Animals with Hierarchical Contrastive Learning
Nolasco, I., Moummad, I., Stowell, D., & Benetos, E. (2025) · IEEE International Conference on Acoustics Speech and Signal Processing · doi:10.1109/icassp49660.2025.10890076 · Cited by 1 · see citing works
“However, this approach restricts the applicability of AIID in real-world settings where multiple species coexist and the set of individuals is not fixed, [4]–[6].”
Compositional Audio Representation Learning
Sridhar, S., & Cartwright, M. (2025) · IEEE International Conference on Acoustics Speech and Signal Processing · doi:10.1109/icassp49660.2025.10890242 · Cited by 1 · see citing works
“This limits machine listening’s potential in applications such as individual ID [2], sound localization, and tracking sound sources at different levels of granularity towards a compositional representation of auditory scenes, as is now commonplace in computer vision [3], [4].”
Self-citationTerritorial Acoustic Species Estimation Using Acoustic Sensor NetworksPreprint
Brüggemann, L., Otten, D., Sachser, F., & Aschenbruck, N. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5123380 · Cited by 1 · see citing works
Listening forward: emerging roles of bioacoustics in ecology, evolution, and conservation
Zsebők, S. (2026) · Biologia Futura · doi:10.1007/s42977-026-00322-5
“The main bottleneck, at least for now, is building and curating reference libraries at a scale that can support global monitoring, along with developing fully automated pipelines that can process such data streams without constant human supervision (Knight et al. 2024; Linhart et al. 2022).”
Territorial Acoustic Species Estimation using Acoustic Sensor NetworksPreprint
Brüggemann, L., Otten, D., Sachser, F., & Aschenbruck, N. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5113322
Acoustic individual identification in a species of field cricket using deep learning
Kabuga, E., Nandi, D., Burrell, S. A., Dlamini, G. S., Balakrishnan, R., Bah, B., & Durbach, I. N. (2026) · The Journal of the Acoustical Society of America · doi:10.1121/10.0044100
Djokic, D. (2025) · Premier Journal of Artificial Intelligence · doi:10.70389/pjai.100017
Tolkova, I., Klinck, H., Cusano, D. A., Kügler, A., & Parks, S. E. (2026) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013321
“Our work contributes to, and closely aligns with, a broader context of acoustic individual identification (AIID) reviewed and conceptually formulated by Knight et al [97].”
Polasik, J. S., Gura, K. B., & Bedrosian, B. E. (2025) · Wildlife Society Bulletin · doi:10.1002/wsb.1616
“Vocalizations of birds are commonly used to identify species (Marler 1958); however, recent advances in bioacoustics allow for the identification of individuals by call differentiation (Terry et al. 2005, Knight et al. 2024).”
Russo, D., Schild, A. B., & Knörnschild, M. (2025) · Scientific Reports · doi:10.1038/s41598-025-31536-7
Morandi, I., Rodriguez, M. A. J., Kwak, M., Petrusková, T., & Linhart, P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.19.695494
“However, identifying individuals from PAM recordings is challenging due to factors such as variation in recording conditions, signal degradation over distance and overlapping calls (Knight et al., 2024).”
InfluentialSinging the night away: diel and seasonal patterns of LeConte's sparrow primary and flight songs
Marsh, A., Hannah, K. C., & Foote, J. R. (2026) · Journal of Avian Biology · doi:10.1002/jav.03625
Best, P., Dassow, A., Kershenbaum, A., Nguyen, T. D., Pogson, M., Maheshwari, A., & Marxer, R. (2026) · PeerJ · doi:10.7717/peerj.20655
Scarpelli, M. D. A., Macdonald, S., Golchin, M., Linke, S., & Froese, J. (2026) · Remote Sensing in Ecology and Conservation · doi:10.1002/rse2.70062
“…al., 2018); PAM devices are less targeted, potentially capturing a large range of taxa as well as contextual information on environmental sounds, and advances in machine learning techniques are making individual 683 recognition using acoustics possible too (Huang et al., 2025; Knight et al., 2024).”
An Open Dataset for the Acoustic Monitoring of Nocturnal Migratory Birds in Europe
Airale, L., Pajot, A., & Linossier, J. (2026) · Scientific Data · doi:10.1038/s41597-026-07176-5
“Indeed, while conspecific calls often overlap and sound similar, subtle individual differences in frequency contours, harmonics, or call timing may still be detectable in the time-frequency domain, allowing for the separation and enumeration of individual callers, even within the same species 44 .”
Automated detection of stereotyped animal sounds using data augmentation and transfer learning
Jancovich, B. A., Sanchez, V., Truong, G., & Rogers, T. L. (2026) · Scientific Reports · doi:10.1038/s41598-026-48308-6
Burton, N. H. K., Kahounová, H., Walker, J. H., Conway, G. J., Robinson, R. A., & Petrusková, T. (2026) · Ibis · doi:10.1111/ibi.70069
Passive Acoustic Monitoring within the Northwest Forest Plan Area: 2025 Annual ReportPreprint
Lesmeister, D. B., Jenkins, J. M. A., Ruff, Z. J., Rugg, N. M., Abidari, S., Beavers, S. C., Christophersen, R. G., Davis, R. J., Terwilliger, M., Henderson, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.26.727992
Self-citationAubin, J. A., Mennill, D. J., Mikus, M., Michaud, R., & Vergara, V. (2026) · Animal Behaviour · doi:10.1016/j.anbehav.2026.123662
Guan, S., Liao, Z., Han, X., & Niu, S. (2026) · iScience · doi:10.1016/j.isci.2026.116422 · Cited by 1 · see citing works
“3,107,108 Figure 5 illustrates this end-to-end work-flow.”
Individual bird identification by modelling temporal structure in bioacoustic embeddings
Gallego-Londoño, J., Martinez-Vargas, J. D., & López, J. D. (2026) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70399
Acoustic remote sensing with deep learning enables non-invasive estimation of seabird nest density
Terranova, F., Todaro, L., Forte, X., Ludynia, K., Geldenhuys, D., Mathevon, N., Reby, D., & Favaro, L. (2026) · Ecological Informatics · doi:10.1016/j.ecoinf.2026.104017
Pérez‐Granados, C., Alonso-Moya, C. D., Barrero, A., Sáez‐Gómez, P., Bota, G., Lahoz‐Monfort, J. J., Laiolo, P., Méndez, M., Serrano, D., Tella, J. L., et al. (2026) · Ecology and Evolution · doi:10.1002/ece3.74380
Dubus, L., Verdier, A., Giotto, N., Mbemba, G., Michelin, G., Mulot, B., Manel, S., & Mouillot, D. (2026) · Remote Sensing in Ecology and Conservation · doi:10.1002/rse2.70110
El monitoreo acústico pasivo como herramienta para estudios de diversidad funcional en aves
Palacio, F. X., Zaffignani, D., & Scheffer, M. (2026) · El Hornero · doi:10.56178/eh.v41i2.1550
Kernan, C. E., Symes, L. B., & ter Hofstede, H. M. (2026) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-026-03815-4
“It is difficult to record and process the large amounts of acoustic data necessary to quantify long-term individual calling effort (Knight et al. 2024; Lengagne et al. 2015), particularly outside of controlled laboratory conditions (though see, e.g., Cade and Cade 1992; Nandi and Balakrishnan 2016;…”
Vocal identification and monitoring of individual Australian Boobook owls ( Ninox boobook )
Jorge, F., Fuller, R. A., & van Rensburg, B. J. (2026) · Bioacoustics · doi:10.1080/09524622.2026.2755343
- Authors
- Knight, E., Rhinehart, T., de Zwaan, D. R., Weldy, M. J., Cartwright, M., Hawley, S. H., Larkin, J. L., Lesmeister, D., Bayne, E., & Kitzes, J.
- Affiliations
- University of Alberta (CA)
- University of Pittsburgh (US)
- Oregon State University (US)
- New Jersey Institute of Technology (US)
- Belmont University (US)
- Indiana University of Pennsylvania (US)
- Corresponding author
- Knight, Elly
- Rhinehart, Tessa
- ORCID
- Venue
- Trends in Ecology & Evolution
- Publisher
- Elsevier BV
- Published
- 2024-10
- Volume
- 39
- Issue
- 10
- Pages
- 947-960
- ISSN
- 0169-5347 (ISSN-L)
- OpenAlex
- W4399561150
- Cited by
- 54
- References
- 100
- Citations by year
- 2026: 30 · 2025: 22 · 2024: 2
- FWCI
- 6.28
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Trends in Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Developmental Biology › Animal Vocal Communication and Behavior
- Physical Sciences › Computer Science › Signal Processing › Music and Audio Processing
- Physical Sciences › Environmental Science › Ecology › Marine animal studies overview
- Keywords
- bioacoustics, deep learning, training data, animal vocalizations
- MeSH terms
- Acoustics, Animals, Vocalization, Animal
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